chemart / chemoton

hub:
  repo_type: generator
  builtin: chemoton
  tags:
  - banzhaf-yamamoto
chemistries:
- id: chemoton
  name: Chemoton
  intuition: 'The classic hand-designed minimal cell, and still the clearest statement of what a cell
    needs. Three subsystems are coupled stoichiometrically: a metabolic cycle that turns nutrient into
    building blocks, a template that replicates using one of those blocks, and a membrane that grows from
    another. Because the couplings are exact, growth and division stay synchronised - the cell divides
    when its membrane has doubled. That tight coupling is also what makes it fragile, which is precisely
    why it is a good stress test.

    '
  origin: Ganti, ~1952/1971
  book: 6.1.4; wet computing 17.4.1
  refs:
  - '[305]'
  - '[306]'
  - '[204]'
  - '[271]'
  - '[604]'
  - '[880]'
  - '[949]'
  - '[273]'
  - '[159]'
  family: origin-of-life
  kind: generator
  constructive: false
  S:
    repr: A1..A5 (metabolic cycle), X (nutrient), Y (waste), V (template monomer), pV0..pV(N-1) (double-stranded
      templates by replication stage), T0 (membrane precursor), T* (activated precursor), T (membrane
      molecule), R (polycondensation by-product), S (membrane surface)
    definition: explicit
  R:
    definition: explicit
    arity:
    - 1
    - 2
    scheme: 'Metabolism A1 + X <-> A2 ; A2 <-> A3 + Y ; A3 <-> A4 + V ; A4 <-> A5 + T0 ; A5 <-> 2 A1.
      Templates pV0 + V <-> pV1 + R (only above [V]*) ; pV_r + V -> pV_(r+1) + R ; pV_(N-1) + V -> 2 pV0
      + R. Membrane T0 -> T* ; T* + R <-> T ; T + S -> 2 S. Division when the surface doubles.

      '
  A:
    reactor:
    - ode
    - compartments
    dilution: cell division halves everything; volume Q = S^1.5
  params:
  - name: N
    type: int
    default: 25
    min: 2
    max: 1000
    role: structural
    meaning: 'template length: monomers bound per replication round, i.e. the number of stages pV0..pV(N-1)'
  - name: X
    type: float
    default: 100.0
    min: 0
    range: the paper also uses 10 and 1
    role: population
    meaning: nutrient concentration outside the cell, held constant
  - name: V_threshold
    type: float
    default: 35.0
    min: 0
    role: kinetic
    meaning: polycondensation threshold [V]*; template initiation pV0 + V -> pV1 + R only runs above it
  - name: rates
    type: dict
    default: {}
    role: kinetic
    meaning: overrides of the paper's rate constants by name (k1..k10 forward, k1r..k6r, k9r reverse);
      unlisted constants keep the paper's values
  provides:
  - topology
  - stoichiometry
  - catalysts
  - rate-constants
  - compartments
  - initial-state
  fidelity: reconstructed
  sources:
  - 'Fernando, C. & Di Paolo, E. (2004). The Chemoton: a model for the origin of long RNA templates. Proc.
    Artificial Life IX. Model I, eqs. 1-14 and appendix. https://ezequieldipaolo.net/wp-content/uploads/2019/09/chemoton.pdf'
  - Csendes, T. (1984). A simulation study on the chemoton. Kybernetes 13:79-85 (source of the metabolic
    equations and rate constants reused above)
  decisions:
  - The book describes the Chemoton only qualitatively. Reactions, rate constants (k1 = 2, k2 = k3 = k4
    = 100, k5 = k6 = k7 = k8 = k9 = k10 = 10, k1r..k5r = 0.1, k6r = 1, k9r = 0.1) and initial conditions
    are model I of Fernando & Di Paolo (2004); each ODE term of their eqs. 1-14 is one mass-action reaction
    (checked in tests).
  - 'Template replication is represented by stage: pV_r is a double strand with r extra monomers bound,
    and binding the last monomer releases two pV0. Initiation only runs while [V] > [V]*; this gate is
    recorded in that reaction''s rate as threshold_species/threshold, since it is not a rate law.'
  - Nutrient X and waste Y are environmental concentrations held constant (extras.buffered; the paper
    sets [X] = 100, [Y] = 0.1). Volume Q = S^1.5 and division at doubled surface act on all concentrations
    rather than as reactions, so they are recorded in extras.compartments.
  - The book's description has T and T' swapped relative to the paper; this entry follows the paper (T0
    precursor, T* activated, T membrane molecule). cycle_size (the paper's wheel is fixed at 5), rate_constants,
    X_influx and division_criterion are replaced by the parameters above.
  phenomena:
  - synchronised growth and division
  - replication time 0.455 at [X] = 100, 0.65 at [X] = 10, 2.4 at [X] = 1 (Fernando & Di Paolo)
  - some robustness to noise and to food shortage
  - differentiation into 'species'
  notes: 'The classic hand-designed minimal cell. Its stoichiometric coupling is exactly what makes it
    fragile, which makes it a good test of any sensitivity-analysis tooling Chemart exports to.

    '